Ok, so I am still waiting for the Ben-Annie storyline to develop and give us more insight into Ben's motivations, but after season 5 it appears that it is not Ben vs. The Universe, but Yin vs. Yang -- Jacob vs. the MIB. I think these guys have to exist in harmony -- balance -- the peace and the chaos -- and what we have seen is the chaos finding a loophole to finally destroy the peace -- but not before the peace can set in motion events that will close that loophole before any major damage can be done.
So here is my most recent theory.
I haven't been following the theories lately, just re-watching seasons 1 and 2, so if I am treading on someone else's ideas, you have my apologies. But this is my theory, and I think it's pretty clear:
What Happened, Happened
No reboot. No alternate timeline. Jughead always exploded. But when you explode an atomic bomb over a pocket of electromagnetic energy, you don't get a normal explosion -- you get "The Incident" which a brilliant guy like Radzinsky can work to contain. That's why the Swan hatch had cement poured over it like Sayid hadn't seen since Chernoble. It's why Desmond told Locke in S2 Finale that the blast doors could even withstand an atomic blast. Jack, Kate, Sawyer, Hurley, Jin -- they will all survive the Incident. But they won't rejoin Dharma and they won't flash back to where they once belonged. They will have to get back to the future the way we all do -- one day at a time -- but they will not age because Jacob's touch "Alpertized" them (they just haven't lived long enough to see that they don't physically age yet) and they will go through their lives from 1977 to 2004 with a foreknowledge of what is to come and a crystal clear understanding that Ms. Hawking is right -- you can't change "the past."
They will be rescued from the angry Dharma mob by Richard Alpert and the hostiles and they will be recruited into the "what lies in shadow of the statue" club. They may even become leaders of this group and will make key, behind-the-scenes moves to set things up for what has to happen -- to the point where they set up many of the things we have already seen in previous seasons: arranging the food-drops; broadcasting the numbers from the radio tower to bring Rousseu to the island; getting Radzinski to paint the flourescent map on the hatch door; splicing the swan orientation video and hiding the missing piece on the other side of the island where they know the tailies will find it; salting the earth around the pearl station to make a "question mark" that Eko can see from the cliff; instructing Ms. Clue to give their names to Michael to bring in exchange for Walt; having the others build a runway for Ajira 316, etc etc etc etc. In other words, they will be setting up a game of moustrap for their younger selves and ensuring that they get where they need to be. I mean, how many times has Lost shown us game-changing presentations of the same event told from different perspectives? This is what it's all about.
In the first half of season six, we will learn that Jack, Kate, Sawyer, Jin, Hurley, and Sayid are the main people setting the stage for the oceanic 815 crash -- even to the point where they 'encourage' and 'manipulate' certain events to get people on the plane who need to be on the plane (even their younger selves). But that's just the first half of Season 6. There is still the overall victory that must be won -- the final battle -- the loophole that must be closed -- the war that must be won. The consequences to Ben's loophole killing of Jacob and the showdown with un-Locke/MIB and whatever else is going on with this mysterious island and the smoke monster and whatnot. The balance between yin (Jacob) and yang (MIB) must be restored, and Jacob has found a way to out-loophole the loophole -- Jack and co. to the rescue ("they're coming...") -- still some surprises to come, I am sure.
My ideal final scene of Lost would be a repeat of the season 5 finale's first scene -- with Jack catching a fish and cooking it on a rock, and Locke coming up to him and saying "do you know how badly I want to kill you?" Jack is the new yin and Locke (or at least the smoke monster in locke's form) is the new yang.
Oh yeah -- one other part of this "What happened, happened" theory -- we will learn that Rose and Bernard are the Adam and Eve skeletons of the caves from season one. I mean we have already seen them hermitting it up in 1977 -- not such a stretch to find them dead and decomposed by 2004. white rock, black rock -- it's pretty obvious, no?